ImmunoGraph MCP

predict_bcell

Read-onlyIdempotent

Scores linear B-cell sequence positions with BepiPred-3.0, Parker hydrophilicity, or GraphBepi, returning residue scores, regions, and provenance for epitope research.

Instructions

Score linear B-cell sequence positions using configured live IEDB BepiPred-3.0, local Parker hydrophilicity, or an exact GraphBepi fixture. Choose the method explicitly: Parker is a physicochemical proxy and GraphBepi is fixture-only in this release. Returns residue scores, regions, and provenance; live IEDB access may fail or time out.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`methods`	Yes	Named predictor methods to run or replay; availability depends on configuration.
`sequence`	No	Protein amino-acid sequence without a FASTA header.
`parameters`	Yes	Method-specific predictor settings; allowed keys depend on selected methods.
`proteinRef`	Yes	Stable protein reference or exact fixture key for this prediction.
`fallbackPolicy`	Yes	Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed7 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / fallbackPolicy / description

Added value: +"Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls."

addedInput schema / properties / methods / description

Added value: +"Named predictor methods to run or replay; availability depends on configuration."

addedInput schema / properties / parameters / description

Added value: +"Method-specific predictor settings; allowed keys depend on selected methods."

addedInput schema / properties / proteinRef / description

Added value: +"Stable protein reference or exact fixture key for this prediction."

addedInput schema / properties / runId / description

Added value: +"Caller-chosen identifier linking this call to one research run."

addedInput schema / properties / sequence / description

Added value: +"Protein amino-acid sequence without a FASTA header."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4.5/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only and idempotent behavior. The description adds useful operational context beyond annotations: live IEDB access may fail or time out, GraphBepi is fixture-only, and results include residue scores, regions, and provenance.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is front-loaded with the core action and method options, then follows with the method caveat and return/provenance note. Every sentence carries useful information without repetition.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the rich schema and output schema, the description provides enough context to call the tool correctly: what it predicts, which methods exist, how they differ, that live access may fail, and what is returned. Parameter details are adequately delegated to the schema.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents all six parameters. The description still adds meaning for the methods parameter by naming BepiPred-3.0, Parker, and GraphBepi and warning about their differing availability and nature.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: score linear B-cell sequence positions. It names the supported prediction methods and clearly distinguishes this B-cell tool from sibling MHC predictors such as predict_mhci and predict_mhcii.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives clear method-selection guidance: choose explicitly, Parker is a physicochemical proxy, GraphBepi is fixture-only, and live IEDB may fail or time out. It does not explicitly state when not to use this tool versus non-predictor siblings, so it falls short of full alternatives guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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